Speed of different Linux distros - why the difference?

This isn't a conclusive answer, just some thoughts that are too long for a comment.

1. Have a try with atop rather than top. It provides a much better view of what's going on. I find the output of top to be very inconsistant these days as well. I have no explanation as to why, but I've seen the same behaviour you have with multiple cores.

2. Are these installs within VMWare by chance? I ran some benchmarks using various tools on 5 different VMs running 5 different distros: Ubuntu, CentOS, RHEL, SUSE and Debian. I got WILDLY differing results that didn't seem to correlate with anything I could find. The advise I received when I escalated this to Red Hat was that some distributions kernels are better optimised for VMWare than others. This was several years ago though so things may have changed.

3. Are you able to better describe the internal benchmark you're running in your app? This question could easily end up sitting between serverfault and stackoverflow...